Deciphering the Evolution of Vertebrate Immune Cell Types with Single-Cell RNA-Seq

  • Santiago J. Carmona
  • David GfellerEmail author


Single-cell RNA-seq is revolutionizing our understanding of the cell type heterogeneity and evolution in many fields of biology, ranging from neuroscience to cancer to immunology. In immunology, one of the main promises of this approach is the ability to define cell types as clusters in the whole transcriptome space (i.e., without relying on specific surface markers), thereby providing an unbiased classification of immune cell types. So far, this technology has been mainly applied in mouse and human. However, technically it could be used for immune cell type identification in any species without requiring the development and validation of species-specific antibodies for cell sorting. Here, we review recent developments using single-cell RNA-seq to characterize immune cell populations in non-mammalian vertebrates, with a focus on zebrafish (Danio rerio). We advocate that single-cell RNA-seq technology is likely to provide key insights into our understanding of the evolution of the adaptive immune system.


  1. Afik S, Yates KB, Bi K, Darko S, Godec J, Gerdemann U, Swadling L, Douek DC, Klenerman P, Barnes EJ et al (2017) Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state. Nucleic Acids Res 45:e148CrossRefPubMedPubMedCentralGoogle Scholar
  2. Andrews TS, Hemberg M (2018) Identifying cell populations with scRNASeq. Mol Aspects Med 59:114–122CrossRefPubMedGoogle Scholar
  3. Arendt D (2005) Genes and homology in nervous system evolution: comparing gene functions, expression patterns, and cell type molecular fingerprints. Theory Biosci Theor Den Biowissenschaften 124:185–197CrossRefGoogle Scholar
  4. Arendt D (2008) The evolution of cell types in animals: emerging principles from molecular studies. Nat Rev Genet 9:868–882CrossRefPubMedGoogle Scholar
  5. Arendt D, Musser JM, Baker CVH, Bergman A, Cepko C, Erwin DH, Pavlicev M, Schlosser G, Widder S, Laubichler MD et al (2016) The origin and evolution of cell types. Nat Rev Genet 17:744–757CrossRefPubMedGoogle Scholar
  6. Athanasiadis EI, Botthof JG, Andres H, Ferreira L, Lio P, Cvejic A (2017) Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis. Nat Commun 8Google Scholar
  7. Binstadt BA, Brumbaugh KM, Leibson PJ (1997) Signal transduction by human NK cell MHC-recognizing receptors. Immunol Rev 155:197–203CrossRefPubMedGoogle Scholar
  8. Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M et al (2011) The evolution of gene expression levels in mammalian organs. Nature 478:343–348CrossRefPubMedGoogle Scholar
  9. Cannon JP, Haire RN, Rast JP, Litman GW (2004) The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms. Immunol Rev 200:12–22CrossRefPubMedGoogle Scholar
  10. Canzar S, Neu KE, Tang Q, Wilson PC, Khan AA (2016) Basic: BCR assembly from single cells. Bioinformatics 631Google Scholar
  11. Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJT, Cvejic A, Gfeller D (2017) Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res 27:451–461CrossRefPubMedPubMedCentralGoogle Scholar
  12. Clark G, Stockinger H, Balderas R, van Zelm MC, Zola H, Hart D, Engel P (2016) Nomenclature of CD molecules from the tenth human leucocyte differentiation antigen workshop. Clin Transl Immunol 5:e57CrossRefGoogle Scholar
  13. Contreras V, Urien C, Guiton R, Alexandre Y, Vu Manh T-P, Andrieu T, Crozat K, Jouneau L, Bertho N, Epardaud M et al (2010) Existence of CD8α-like dendritic cells with a conserved functional specialization and a common molecular signature in distant mammalian species. J Immunol Baltim Md 1950(185):3313–3325Google Scholar
  14. Cooper MD, Alder MN (2006) The evolution of adaptive immune systems. Cell 124:815–822CrossRefGoogle Scholar
  15. Cooper MD, Peterson RD, Good RA (1965) Delineation of the thymic and bursal lymphoid systems in the chicken. Nature 205:143–146CrossRefPubMedGoogle Scholar
  16. Cooper MD, Raymond DA, Peterson RD, South MA, Good RA (1966) The functions of the thymus system and the bursa system in the chicken. J Exp Med 123:75–102CrossRefPubMedPubMedCentralGoogle Scholar
  17. Crozat K, Guiton R, Guilliams M, Henri S, Baranek T, Schwartz-Cornil I, Malissen B, Dalod M (2010) Comparative genomics as a tool to reveal functional equivalences between human and mouse dendritic cell subsets. Immunol Rev 234:177–198CrossRefPubMedGoogle Scholar
  18. Davidson AJ, Zon LI (2004) The “definitive” (and ‘primitive’) guide to zebrafish hematopoiesis. Oncogene 23:7233–7246CrossRefPubMedGoogle Scholar
  19. Eltahla AA, Rizzetto S, Pirozyan MR, Betz-Stablein BD, Venturi V, Kedzierska K, Lloyd AR, Bull RA, Luciani F (2016) Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells. Immunol Cell Biol 94:604–611CrossRefPubMedGoogle Scholar
  20. Flajnik MF, Kasahara M (2010) Origin and evolution of the adaptive immune system: genetic events and selective pressures. Nat Rev Genet 11:47–59CrossRefPubMedGoogle Scholar
  21. Francis WR, Christianson LM, Kiko R, Powers ML, Shaner NC, Haddock SH (2013) A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genom 14:167CrossRefGoogle Scholar
  22. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652CrossRefPubMedPubMedCentralGoogle Scholar
  23. Guillaumet-Adkins A, Rodríguez-Esteban G, Mereu E, Mendez-Lago M, Jaitin DA, Villanueva A, Vidal A, Martinez-Marti A, Felip E, Vivancos A et al (2017) Single-cell transcriptome conservation in cryopreserved cells and tissues. Genome Biol 18Google Scholar
  24. Haire RN, Cannon JP, O’Driscoll ML, Ostrov DA, Mueller MG, Turner PM, Litman RT, Litman GW, Yoder JA (2012) Genomic and functional characterization of the diverse immunoglobulin domain-containing protein (DICP) family. Genomics 99:282–291CrossRefPubMedPubMedCentralGoogle Scholar
  25. Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O et al (2016) CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol 17Google Scholar
  26. Hirano M, Guo P, McCurley N, Schorpp M, Das S, Boehm T, Cooper MD (2013) Evolutionary implications of a third lymphocyte lineage in lampreys. Nature 501:435–438CrossRefPubMedPubMedCentralGoogle Scholar
  27. Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L et al (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498–503CrossRefPubMedPubMedCentralGoogle Scholar
  28. Inoue T, Moritomo T, Tamura Y, Mamiya S, Fujino H, Nakanishi T (2002) A new method for fish leucocyte counting and partial differentiation by flow cytometry. Fish Shellfish Immunol 13:379–390CrossRefPubMedGoogle Scholar
  29. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S (2014) Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods 11:163–166CrossRefPubMedGoogle Scholar
  30. Jacobson G, Muncaster S, Mensink K, Forlenza M, Elliot N, Broomfield G, Signal B, Bird S (2017) Omics and cytokine discovery in fish: presenting the Yellowtail kingfish (Seriola lalandi) as a case study. Dev Comp Immunol 75:63–76CrossRefPubMedGoogle Scholar
  31. Ji P, Liu G, Xu J, Wang X, Li J, Zhao Z, Zhang X, Zhang Y, Xu P, Sun X (2012) Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics. PLoS ONE 7:e35152CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kasheta M, Painter CA, Moore FE, Lobbardi R, Bryll A, Freiman E, Stachura D, Rogers AB, Houvras Y, Langenau DM et al (2017) Identification and characterization of T reg-like cells in zebrafish. J Exp Med 214:3519–3530CrossRefPubMedPubMedCentralGoogle Scholar
  33. Kiessling R, Klein E, Wigzell H (1975) “Natural” killer cells in the mouse. I. Cytotoxic cells with specificity for mouse Moloney leukemia cells. Specificity and distribution according to genotype. Eur J Immunol 5:112–117CrossRefPubMedGoogle Scholar
  34. Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA (2015) The technology and biology of single-cell RNA sequencing. Mol Cell 58:610–620CrossRefPubMedGoogle Scholar
  35. Langenau DM, Ferrando AA, Traver D, Kutok JL, Hezel J-PD, Kanki JP, Zon LI, Look AT, Trede NS (2004) In vivo tracking of T cell development, ablation, and engraftment in transgenic zebrafish. Proc Natl Acad Sci 101:7369–7374CrossRefPubMedGoogle Scholar
  36. Liao X, Cheng L, Xu P, Lu G, Wachholtz M, Sun X, Chen S (2013) Transcriptome analysis of crucian carp (Carassius auratus), an important aquaculture and hypoxia-tolerant species. PLoS ONE 8:e62308CrossRefPubMedPubMedCentralGoogle Scholar
  37. Lin H-F (2005) Analysis of thrombocyte development in CD41-GFP transgenic zebrafish. Blood 106:3803–3810CrossRefPubMedPubMedCentralGoogle Scholar
  38. Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Nair AS, Liligeto UN et al (2017) Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria. Sci Immunol 2:eaal2192Google Scholar
  39. Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F, Voet T, Teichmann SA, Cvejic A (2016) Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells. Cell Rep 14:966–977CrossRefPubMedPubMedCentralGoogle Scholar
  40. Manh T-PV, Alexandre Y, Baranek T, Crozat K, Dalod M (2013) Plasmacytoid, conventional, and monocyte-derived dendritic cells undergo a profound and convergent genetic reprogramming during their maturation. Eur J Immunol 43:1706–1715CrossRefPubMedGoogle Scholar
  41. Marioni JC, Arendt D (2017) How single-cell genomics is changing evolutionary and developmental biology. Annu Rev Cell Dev Biol 33:537–553CrossRefPubMedGoogle Scholar
  42. Martin SAM, Król E (2017) Nutrigenomics and immune function in fish: new insights from omics technologies. Dev Comp Immunol 75:86–98CrossRefPubMedPubMedCentralGoogle Scholar
  43. Mathias JR, Perrin BJ, Liu T-X, Kanki J, Look AT, Huttenlocher A (2006) Resolution of inflammation by retrograde chemotaxis of neutrophils in transgenic zebrafish. J Leukoc Biol 80:1281–1288CrossRefPubMedGoogle Scholar
  44. Mebius RE, Rennert P, Weissman IL (1997) Developing lymph nodes collect CD4 + CD3-LT beta + cells that can differentiate to APC, NK cells, and follicular cells but not T or B cells. Immunity 7:493–504CrossRefPubMedGoogle Scholar
  45. Moore FE, Garcia EG, Lobbardi R, Jain E, Tang Q, Moore JC, Cortes M, Molodtsov A, Kasheta M, Luo CC et al (2016) Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish. J Exp Med 213:979–992CrossRefPubMedPubMedCentralGoogle Scholar
  46. Morales Poole JR, Paganini J, Pontarotti P (2017) Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: an evolutionary biology approach based study. Dev Comp Immunol 75:120–126CrossRefPubMedGoogle Scholar
  47. Mora-Velandia LM, Castro-Escamilla O, Méndez AG, Aguilar-Flores C, Velázquez-Avila M, Tussié-Luna MI, Téllez-Sosa J, Maldonado-García C, Jurado-Santacruz F, Ferat-Osorio E et al (2017) A human Lin CD123 + CD127 low population endowed with ILC features and migratory capabilities contributes to immunopathological hallmarks of psoriasis. Front Immunol 8:176CrossRefPubMedPubMedCentralGoogle Scholar
  48. Notta F, Zandi S, Takayama N, Dobson S, Gan OI, Wilson G, Kaufmann KB, McLeod J, Laurenti E, Dunant CF et al (2016) Distinct routes of lineage development reshape the human blood hierarchy across ontogeny. Science 351:aab2116–aab2116Google Scholar
  49. Page DM, Wittamer V, Bertrand JY, Lewis KL, Pratt DN, Delgado N, Schale SE, McGue C, Jacobsen BH, Doty A et al (2013) An evolutionarily conserved program of B-cell development and activation in zebrafish. Blood 122:e1–e11CrossRefPubMedPubMedCentralGoogle Scholar
  50. Pancer Z, Amemiya CT, Ehrhardt GRA, Ceitlin J, Larry Gartland G, Cooper MD (2004) Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430:174–180CrossRefGoogle Scholar
  51. Papalexi E, Satija R (2017) Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol 18:35–45CrossRefPubMedGoogle Scholar
  52. Paul F, Arkin Y, Giladi A, Jaitin DA, Kenigsberg E, Keren-Shaul H, Winter D, Lara-Astiaso D, Gury M, Weiner A et al (2015) Transcriptional heterogeneity and lineage commitment in myeloid progenitors. Cell 163:1663–1677CrossRefPubMedGoogle Scholar
  53. Pereiro P, Varela M, Diaz-Rosales P, Romero A, Dios S, Figueras A, Novoa B (2015) Zebrafish Nk-lysins: first insights about their cellular and functional diversification. Dev Comp Immunol 51:148–159CrossRefPubMedGoogle Scholar
  54. Picelli S, Faridani OR, Björklund ÅK, Winberg G, Sagasser S, Sandberg R (2014) Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9:171–181CrossRefPubMedGoogle Scholar
  55. Pierrard M-A, Roland K, Kestemont P, Dieu M, Raes M, Silvestre F (2012) Fish peripheral blood mononuclear cells preparation for future monitoring applications. Anal Biochem 426:153–165CrossRefPubMedGoogle Scholar
  56. Psaila B, Barkas N, Iskander D, Roy A, Anderson S, Ashley N, Caputo VS, Lichtenberg J, Loaiza S, Bodine DM et al (2016) Single-cell profiling of human megakaryocyte-erythroid progenitors identifies distinct megakaryocyte and erythroid differentiation pathways. Genome Biol 17Google Scholar
  57. Raj A, van Oudenaarden A (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135:216–226CrossRefPubMedPubMedCentralGoogle Scholar
  58. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M et al (2017) The human cell Atlas. ELife 6 Google Scholar
  59. Renshaw SA, Trede NS (2012) A model 450 million years in the making: zebrafish and vertebrate immunity. Dis Model Mech 5:38–47CrossRefPubMedPubMedCentralGoogle Scholar
  60. Renshaw SA, Loynes CA, Trushell DMI, Elworthy S, Ingham PW, Whyte MKB (2006) A transgenic zebrafish model of neutrophilic inflammation. Blood 108:3976–3978CrossRefPubMedGoogle Scholar
  61. Rey Vázquez G, Guerrero GA (2007) Characterization of blood cells and hematological parameters in Cichlasoma dimerus (Teleostei, Perciformes). Tissue Cell 39:151–160CrossRefPubMedGoogle Scholar
  62. Rhee J-S, Jeong C-B, Kim D-H, Kim I-C, Lee YS, Lee C, Lee J-S (2014) Immune gene discovery in the crucian carp Carassius auratus. Fish Shellfish Immunol 36:240–251CrossRefPubMedGoogle Scholar
  63. Robbins SH, Walzer T, Dembélé D, Thibault C, Defays A, Bessou G, Xu H, Vivier E, Sellars M, Pierre P et al (2008) Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling. Genome Biol 9:R17CrossRefPubMedPubMedCentralGoogle Scholar
  64. Rougeot J, Zakrzewska A, Kanwal Z, Jansen HJ, Spaink HP, Meijer AH (2014) RNA sequencing of FACS-sorted immune cell populations from zebrafish infection models to identify cell specific responses to intracellular pathogens. Methods Mol Biol Clifton NJ 1197:261–274CrossRefGoogle Scholar
  65. Saraceni PR, Romero A, Figueras A, Novoa B (2016) Establishment of infection models in zebrafish larvae (Danio rerio) to study the pathogenesis of aeromonas hydrophila. Front Microbiol 7:1219CrossRefPubMedPubMedCentralGoogle Scholar
  66. Schlitzer A, Sivakamasundari V, Chen J, Sumatoh HRB, Schreuder J, Lum J, Malleret B, Zhang S, Larbi A, Zolezzi F et al (2015) Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow. Nat Immunol 16:718–728CrossRefPubMedGoogle Scholar
  67. Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinform Oxf Engl 28:1086–1092CrossRefGoogle Scholar
  68. Spits H, Artis D, Colonna M, Diefenbach A, Di Santo JP, Eberl G, Koyasu S, Locksley RM, McKenzie ANJ, Mebius RE et al (2013) Innate lymphoid cells—a proposal for uniform nomenclature. Nat Rev Immunol 13:145–149CrossRefPubMedGoogle Scholar
  69. Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA (2016) T cell fate and clonality inference from single-cell transcriptomes. Nat Methods 13:329–332CrossRefPubMedPubMedCentralGoogle Scholar
  70. Stubbington MJT, Rozenblatt-Rosen O, Regev A, Teichmann SA (2017) Single-cell transcriptomics to explore the immune system in health and disease. Science 358:58–63CrossRefPubMedPubMedCentralGoogle Scholar
  71. Sudhagar A, Kumar G, El-Matbouli M (2018) Transcriptome analysis based on RNA-seq in understanding pathogenic mechanisms of diseases and the immune system of fish: a comprehensive review. Int J Mol, Sci 19Google Scholar
  72. Suffiotti M, Carmona SJ, Jandus C, Gfeller D (2017) Identification of innate lymphoid cells in single-cell RNA-Seq data. Immunogenetics 69:439–450CrossRefPubMedGoogle Scholar
  73. Svensson V, Vento-Tormo R, Teichmann SA (2018) Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc 13:599–604CrossRefPubMedGoogle Scholar
  74. Tamplin OJ, Durand EM, Carr LA, Childs SJ, Hagedorn EJ, Li P, Yzaguirre AD, Speck NA, Zon LI (2015) Hematopoietic stem cell arrival triggers dynamic remodeling of the perivascular niche. Cell 160:241–252CrossRefPubMedPubMedCentralGoogle Scholar
  75. Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML et al (2017) Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med 214:2875–2887CrossRefPubMedPubMedCentralGoogle Scholar
  76. Tokunaga Y, Shirouzu M, Sugahara R, Yoshiura Y, Kiryu I, Ototake M, Nagasawa T, Somamoto T, Nakao M (2017) Comprehensive validation of T- and B-cell deficiency in rag1-null zebrafish: implication for the robust innate defense mechanisms of teleosts. Sci Rep 7Google Scholar
  77. Trapnell C (2015) Defining cell types and states with single-cell genomics. Genome Res 25:1491–1498CrossRefPubMedPubMedCentralGoogle Scholar
  78. Traver D, Paw BH, Poss KD, Penberthy WT, Lin S, Zon LI (2003) Transplantation and in vivo imaging of multilineage engraftment in zebrafish bloodless mutants. Nat Immunol 4:1238–1246CrossRefPubMedGoogle Scholar
  79. Udvadia AJ, Linney E (2003) Windows into development: historic, current, and future perspectives on transgenic zebrafish. Dev Biol 256:1–17CrossRefPubMedGoogle Scholar
  80. Villani A-C, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S et al (2017) Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356Google Scholar
  81. Vivier E, van de Pavert SA, Cooper MD, Belz GT (2016) The evolution of innate lymphoid cells. Nat Immunol 17:790–794CrossRefPubMedPubMedCentralGoogle Scholar
  82. Vu Manh T-P, Marty H, Sibille P, Le Vern Y, Kaspers B, Dalod M, Schwartz-Cornil I, Quéré P (2014) Existence of conventional dendritic cells in Gallus gallus revealed by comparative gene expression profiling. J Immunol Baltim Md 1950(192):4510–4517Google Scholar
  83. Vu Manh T-P, Elhmouzi-Younes J, Urien C, Ruscanu S, Jouneau L, Bourge M, Moroldo M, Foucras G, Salmon H, Marty H et al (2015) Defining mononuclear phagocyte subset homology across several distant warm-blooded vertebrates through comparative transcriptomics. Front Immunol 6:299PubMedPubMedCentralGoogle Scholar
  84. Warner NL, Szenberg A, Burnet FM (1962) The immunological role of different lymphoid organs in the chicken. I. Dissociation of immunological responsiveness. Aust J Exp Biol Med Sci 40:373–387CrossRefPubMedGoogle Scholar
  85. Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W, Yuan H, Bian C, Lu J, He S et al (2016) The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol 14:1CrossRefPubMedPubMedCentralGoogle Scholar
  86. Yoder JA, Litman RT, Mueller MG, Desai S, Dobrinski KP, Montgomery JS, Buzzeo MP, Ota T, Amemiya CT, Trede NS et al (2004) Resolution of the novel immune-type receptor gene cluster in zebrafish. Proc Natl Acad Sci 101:15706–15711CrossRefPubMedGoogle Scholar
  87. Zapata A, Amemiya CT (2000) Phylogeny of lower vertebrates and their immunological structures. Curr Top Microbiol Immunol 248:67–107PubMedGoogle Scholar
  88. Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J et al (2017) Massively parallel digital transcriptional profiling of single cells. Nat Commun 8:14049CrossRefPubMedPubMedCentralGoogle Scholar
  89. Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L (2016) Single-cell barcoding and sequencing using droplet microfluidics. Nat Protoc 12:44–73CrossRefPubMedGoogle Scholar
  90. Iwama G, Nakanishi, T (1996) Fish physiology, vol. 15: The fish immune system: organism, pathogen and environment. Academic Press, New YorkGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of OncologyLudwig Institute for Cancer Research, University of LausanneLausanneSwitzerland
  2. 2.Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland

Personalised recommendations